def to_ieee_754(R):
"""Convert and return the rotation matrix as the full precision IEEE 754 byte array."""
array = []
for i in range(3):
array.append([])
for j in range(3):
array[i].append(floatAsByteArray(R[i, j]))
return array
def to_ieee_754(R):
"""Convert and return the rotation matrix as the full precision IEEE 754 byte array."""
array = []
for i in range(3):
array.append([])
for j in range(3):
array[i].append(floatAsByteArray(R[i, j]))
return array
def object_to_xml(doc, elem, value=None):
"""Convert the given value into an XML form.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param elem: The element to add the Python objects to.
@type elem: XML element object
@keyword value: The Python object to convert.
@type value: anything
"""
# Add the text value to the sub element.
val_elem = doc.createElement('value')
elem.appendChild(val_elem)
val_elem.appendChild(doc.createTextNode(repr(value)))
# The object type.
if value is None:
py_type = 'None'
elif isinstance(value, bool):
py_type = 'bool'
elif isinstance(value, str) or isinstance(value, unicode):
py_type = 'str'
elif isinstance(value, float):
py_type = 'float'
elif isinstance(value, int):
py_type = 'int'
elif isinstance(value, list):
py_type = 'list'
elif isinstance(value, dict):
py_type = 'dict'
elif isinstance(value, ndarray):
py_type = repr(value.dtype)
else:
raise RelaxError("Unknown type for the value %s." % repr(value))
# Store as an attribute.
elem.setAttribute('type', py_type)
# Store floats as IEEE-754 byte arrays (for full precision storage).
if lib.check_types.is_float(value):
val_elem = doc.createElement('ieee_754_byte_array')
elem.appendChild(val_elem)
val_elem.appendChild(doc.createTextNode(repr(floatAsByteArray(value))))
# Store lists with floats as IEEE-754 byte arrays.
elif (isinstance(value, list) or isinstance(value, ndarray)) and len(value) and lib.check_types.is_float(value[0]):
# The converted list.
ieee_obj = []
conv = False
for i in range(len(value)):
# A float.
if lib.check_types.is_float(value[i]):
ieee_obj.append(floatAsByteArray(value[i]))
conv = True
# All other data.
else:
ieee_obj.append(value)
# Store as XML.
if conv:
# The element.
val_elem = doc.createElement('ieee_754_byte_array')
elem.appendChild(val_elem)
# Add the text.
val_elem.appendChild(doc.createTextNode(repr(ieee_obj)))
# Store dictionaries with floats as IEEE-754 byte arrays.
elif py_type == 'dict':
# The converted dict.
ieee_obj = {}
conv = False
for key in value:
if lib.check_types.is_float(value[key]):
ieee_obj[key] = floatAsByteArray(value[key])
conv = True
# Store as XML.
if conv:
# The element.
val_elem = doc.createElement('ieee_754_byte_array')
elem.appendChild(val_elem)
# Add the text.
val_elem.appendChild(doc.createTextNode(repr(ieee_obj)))
# Store matrices of floats as IEEE-754 byte arrays.
elif lib.arg_check.is_float_matrix(value, none_elements=True, raise_error=False):
# The converted list.
ieee_obj = []
for i in range(len(value)):
# Handle None elements.
if value[i] is None:
ieee_obj.append(None)
continue
# A normal float list or numpy array.
ieee_obj.append([])
for j in range(len(value[i])):
ieee_obj[-1].append(floatAsByteArray(value[i][j]))
# The element.
val_elem = doc.createElement('ieee_754_byte_array')
elem.appendChild(val_elem)
# Add the text.
val_elem.appendChild(doc.createTextNode(repr(ieee_obj)))
def object_to_xml(doc, elem, value=None):
"""Convert the given value into an XML form.
@param doc: The XML document object.
@type doc: xml.dom.minidom.Document instance
@param elem: The element to add the Python objects to.
@type elem: XML element object
@keyword value: The Python object to convert.
@type value: anything
"""
# Add the text value to the sub element.
val_elem = doc.createElement('value')
elem.appendChild(val_elem)
val_elem.appendChild(doc.createTextNode(repr(value)))
# The object type.
if value == None:
py_type = 'None'
elif isinstance(value, bool):
py_type = 'bool'
elif isinstance(value, str):
py_type = 'str'
elif isinstance(value, float):
py_type = 'float'
elif isinstance(value, int):
py_type = 'int'
elif isinstance(value, list):
py_type = 'list'
elif isinstance(value, dict):
py_type = 'dict'
elif isinstance(value, ndarray):
py_type = repr(value.dtype)
else:
raise RelaxError("Unknown type for the value '%s'." % value)
# Store as an attribute.
elem.setAttribute('type', py_type)
# Store floats as IEEE-754 byte arrays (for full precision storage).
if lib.check_types.is_float(value):
val_elem = doc.createElement('ieee_754_byte_array')
elem.appendChild(val_elem)
val_elem.appendChild(doc.createTextNode(repr(floatAsByteArray(value))))
# Store lists with floats as IEEE-754 byte arrays.
elif (isinstance(value, list) or isinstance(value, ndarray)) and len(value) and lib.check_types.is_float(value[0]):
# The converted list.
ieee_obj = []
conv = False
for i in range(len(value)):
# A float.
if lib.check_types.is_float(value[i]):
ieee_obj.append(floatAsByteArray(value[i]))
conv = True
# All other data.
else:
ieee_obj.append(value)
# Store as XML.
if conv:
# The element.
val_elem = doc.createElement('ieee_754_byte_array')
elem.appendChild(val_elem)
# Add the text.
val_elem.appendChild(doc.createTextNode(repr(ieee_obj)))
# Store dictionaries with floats as IEEE-754 byte arrays.
elif py_type == 'dict':
# The converted dict.
ieee_obj = {}
conv = False
for key in list(value.keys()):
if lib.check_types.is_float(value[key]):
ieee_obj[key] = floatAsByteArray(value[key])
conv = True
# Store as XML.
if conv:
# The element.
val_elem = doc.createElement('ieee_754_byte_array')
elem.appendChild(val_elem)
# Add the text.
val_elem.appendChild(doc.createTextNode(repr(ieee_obj)))
# Store matrices of floats as IEEE-754 byte arrays.
elif lib.arg_check.is_float_matrix(value, raise_error=False):
# The converted list.
ieee_obj = []
for i in range(len(value)):
ieee_obj.append([])
for j in range(len(value[i])):
ieee_obj[-1].append(floatAsByteArray(value[i][j]))
# The element.
val_elem = doc.createElement('ieee_754_byte_array')
elem.appendChild(val_elem)
# Add the text.
val_elem.appendChild(doc.createTextNode(repr(ieee_obj)))
def convergence(self):
"""Test for the convergence of the global model."""
# Print out.
print("\n\n\n")
print("#####################")
print("# Convergence tests #")
print("#####################\n")
# Maximum number of iterations reached.
if self.max_iter and self.round > self.max_iter:
print("Maximum number of global iterations reached. Terminating the protocol before convergence has been reached.")
return True
# Store the data of the current data pipe.
self.conv_data.chi2.append(cdp.chi2)
# Create a string representation of the model-free models of the current data pipe.
curr_models = ''
for spin in spin_loop():
if hasattr(spin, 'model'):
if not spin.model == 'None':
curr_models = curr_models + spin.model
self.conv_data.models.append(curr_models)
# Store the diffusion tensor parameters.
self.conv_data.diff_vals.append([])
for param in self.conv_data.diff_params:
# Get the parameter values.
self.conv_data.diff_vals[-1].append(getattr(cdp.diff_tensor, param))
# Store the model-free parameters.
self.conv_data.mf_vals.append([])
self.conv_data.mf_params.append([])
self.conv_data.spin_ids.append([])
for spin, spin_id in spin_loop(return_id=True):
# Skip spin systems with no 'params' object.
if not hasattr(spin, 'params'):
continue
# Add the spin ID, parameters, and empty value list.
self.conv_data.spin_ids[-1].append(spin_id)
self.conv_data.mf_params[-1].append([])
self.conv_data.mf_vals[-1].append([])
# Loop over the parameters.
for j in range(len(spin.params)):
# Get the parameters and values.
self.conv_data.mf_params[-1][-1].append(spin.params[j])
self.conv_data.mf_vals[-1][-1].append(getattr(spin, spin.params[j].lower()))
# No need for tests.
if self.round == 1:
print("First round of optimisation, skipping the convergence tests.\n\n\n")
return False
# Loop over the iterations.
converged = False
for i in range(self.start_round, self.round - 1):
# Print out.
print("\n\n\n# Comparing the current iteration to iteration %i.\n" % (i+1))
# Index.
index = i - self.start_round
# Chi-squared test.
print("Chi-squared test:")
print(" chi2 (iter %i): %s" % (i+1, self.conv_data.chi2[index]))
print(" (as an IEEE-754 byte array: %s)" % floatAsByteArray(self.conv_data.chi2[index]))
print(" chi2 (iter %i): %s" % (self.round, self.conv_data.chi2[-1]))
print(" (as an IEEE-754 byte array: %s)" % floatAsByteArray(self.conv_data.chi2[-1]))
print(" chi2 (difference): %s" % (self.conv_data.chi2[index] - self.conv_data.chi2[-1]))
if self.conv_data.chi2[index] == self.conv_data.chi2[-1]:
print(" The chi-squared value has converged.\n")
else:
print(" The chi-squared value has not converged.\n")
continue
# Identical model-free model test.
print("Identical model-free models test:")
if self.conv_data.models[index] == self.conv_data.models[-1]:
print(" The model-free models have converged.\n")
else:
print(" The model-free models have not converged.\n")
continue
# Identical diffusion tensor parameter value test.
print("Identical diffusion tensor parameter test:")
params_converged = True
for k in range(len(self.conv_data.diff_params)):
# Test if not identical.
if self.conv_data.diff_vals[index][k] != self.conv_data.diff_vals[-1][k]:
print(" Parameter: %s" % param)
print(" Value (iter %i): %s" % (i+1, self.conv_data.diff_vals[index][k]))
print(" (as an IEEE-754 byte array: %s)" % floatAsByteArray(self.conv_data.diff_vals[index][k]))
print(" Value (iter %i): %s" % (self.round, self.conv_data.diff_vals[-1][k]))
print(" (as an IEEE-754 byte array: %s)" % floatAsByteArray(self.conv_data.diff_vals[-1][k]))
print(" The diffusion parameters have not converged.\n")
params_converged = False
break
if not params_converged:
continue
print(" The diffusion tensor parameters have converged.\n")
# Identical model-free parameter value test.
print("\nIdentical model-free parameter test:")
if len(self.conv_data.spin_ids[index]) != len(self.conv_data.spin_ids[-1]):
print(" Different number of spins.")
continue
for j in range(len(self.conv_data.spin_ids[-1])):
# Loop over the parameters.
for k in range(len(self.conv_data.mf_params[-1][j])):
# Test if not identical.
if self.conv_data.mf_vals[index][j][k] != self.conv_data.mf_vals[-1][j][k]:
print(" Spin ID: %s" % self.conv_data.spin_ids[-1][j])
print(" Parameter: %s" % self.conv_data.mf_params[-1][j][k])
print(" Value (iter %i): %s" % (i+1, self.conv_data.mf_vals[index][j][k]))
print(" (as an IEEE-754 byte array: %s)" % floatAsByteArray(self.conv_data.mf_vals[index][j][k]))
print(" Value (iter %i): %s" % (self.round, self.conv_data.mf_vals[-1][j][k]))
print(" (as an IEEE-754 byte array: %s)" % floatAsByteArray(self.conv_data.mf_vals[index][j][k]))
print(" The model-free parameters have not converged.\n")
params_converged = False
break
if not params_converged:
continue
print(" The model-free parameters have converged.\n")
# Convergence.
converged = True
break
# Final printout.
##################
print("\nConvergence:")
if converged:
# Update the status.
status.auto_analysis[self.pipe_bundle].convergence = True
# Print out.
print(" [ Yes ]")
# Return the termination condition.
return True
else:
# Print out.
print(" [ No ]")
# Return False to not terminate.
return False
PIVOT = array([ 37.254, 0.5, 16.7465])
R_PIVOT = zeros((3, 3), float64)
TORSION_ANGLE = 100 / 3.0
COM_C = array([ 26.83678091, -12.37906417, 28.34154128])
R_TORSION = zeros((3, 3), float64)
VECT_TORSION = COM_C - PIVOT
VECT_TORSION = VECT_TORSION / norm(VECT_TORSION)
# Generate a random pivot rotation.
R_random_axis(R_PIVOT, PIVOT_ANGLE)
# Print out.
print("\nThe pivot rotation angle is: %20.40f" % PIVOT_ANGLE)
print("The pivot rotation angle is: %s" % floatAsByteArray(PIVOT_ANGLE))
print("\nThe pivot rotation matrix is:\n%s" % R_PIVOT)
print("Or:")
float_array = to_ieee_754(R_PIVOT)
for i in range(3):
print(float_array[i])
# Generate the torsion angle rotation.
axis_angle_to_R(VECT_TORSION, TORSION_ANGLE, R_TORSION)
# Print out.
print("\nThe torsion rotation matrix is:\n%s" % R_TORSION)
print("Or:")
float_array = to_ieee_754(R_TORSION)
for i in range(3):
print(float_array[i])
PIVOT = array([ 37.254, 0.5, 16.7465])
R_PIVOT = zeros((3, 3), float64)
TORSION_ANGLE = 100 / 3.0
COM_C = array([ 26.83678091, -12.37906417, 28.34154128])
R_TORSION = zeros((3, 3), float64)
VECT_TORSION = COM_C - PIVOT
VECT_TORSION = VECT_TORSION / norm(VECT_TORSION)
# Generate a random pivot rotation.
R_random_axis(R_PIVOT, PIVOT_ANGLE)
# Print out.
print("\nThe pivot rotation angle is: %20.40f" % PIVOT_ANGLE)
print("The pivot rotation angle is: %s" % floatAsByteArray(PIVOT_ANGLE))
print("\nThe pivot rotation matrix is:\n%s" % R_PIVOT)
print("Or:")
float_array = to_ieee_754(R_PIVOT)
for i in range(3):
print(float_array[i])
# Generate the torsion angle rotation.
axis_angle_to_R(VECT_TORSION, TORSION_ANGLE, R_TORSION)
# Print out.
print("\nThe torsion rotation matrix is:\n%s" % R_TORSION)
print("Or:")
float_array = to_ieee_754(R_TORSION)
for i in range(3):
print(float_array[i])
